GSM4733289: HDAC3 ChIP R1881 rep3; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
TFs and others
Antigen
HDAC3
Cell type
Cell type Class
Digestive tract
Cell type
KYSE-410
Primary Tissue
Esophagus
Tissue Diagnosis
Carcinoma Squamous Cell
Attributes by original data submitter
Sample
source_name
human esophagus
cell line
ESCC cell line KYSE410
disease state
esophageal squamous cell carcinoma
treatment
R1881, 4h
chip antibody
HDAC3 Polyclonal Antibody (PA5-85378) from Invitrogen
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, cells were crosslinked with 1% formaldehyde for 10 min on horizontal rotator at room temperature and cell pellets were collected and subjected to sonication. The sheared chromatin was then diluted and immunoprecipitated with 4 µg of specific antibodies at 4°C overnight. After washing, chromatin complexes were eluted with elution buffer and crosslinking was reversed at 65°C overnight. DNA fragments were purified with the QIAquick PCR purification kit. For RNA-seq, total RNA was isolated using an RNeasy kit (QIAGEN). Next, mRNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module. After two rounds of processes, the mRNA was recovered for library generation. For ChIP-seq, the eluted ChIP DNA was used for library preparation with NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina according to the manufacturer's protocol. The library was amplified with 12 PCR cycles and prepared with gel-based size selection. For RNA-seq, the library preparation was performed with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina following the manufacturer's instructions. The cDNA molecules were amplified by 8 cycles of PCR. Non-size selection libraries were then sequenced for using Illumina HiSeq 4000 at the Duke sequencing core.